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Sample GSM1277368 Query DataSets for GSM1277368
Status Public on Dec 03, 2013
Title ZebrafishEmbyos_Control~72_rep2
Sample type RNA
 
Source name ZebrafishEmbyos, Control, Sac 72hpf
Organism Danio rerio
Characteristics tissue: Zebrafish embyos
treatment: control
age: 72 hours post fertilization
Treatment protocol ZFE were exposed continuously for 48 hours to 250mg of emulsions that had been “buttered” on the bottom of cups, to which 30 ZFE and 100 ml of zebrafish medium were added. ZFE were exposed from 0-48, 24-72 or 48-96 hr post-fertilization. RNA samples collected from all exposed and control groups were hybridized to Affymetrix zebrafish microarrays. We extracted RNA from all 30 ZFE in each cup for microarray analysis.
Growth protocol Adult zebrafish were bred the night before exposure date and the embryos were transferred into new containers (plastic storage container) with fresh, aerated, 28°C egg medium.
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed according to the manufacturer's instructions (QIAGEN).
Label biotin
Label protocol Processed according to the manufacturer's protocol in Lousiana State University Health and Science Center-Shreveport
 
Hybridization protocol Processed according to the manufacturer's protocol in Lousiana State University Health and Science Center-Shreveport
Scan protocol Processed according to the manufacturer's protocol in Lousiana State University Health and Science Center-Shreveport
Description ZebrafishEmbyos, Control, Sac 72hpf
Data processing The data were analyzed with R/bioconductor platform. Results were standardized with RMA (Robust Multiarray Average) method.
 
Submission date Dec 02, 2013
Last update date Dec 03, 2013
Contact name Rui Xiao
E-mail(s) ruixiao85@gmail.com
Organization name Columbia University
Department Anesthesiology
Lab P&S 12-402
Street address 630 West 168th Street
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL1319
Series (1)
GSE52873 Microarray data from zebrafish embryos (ZFE) exposed for 48-hr periods to oil emulsions collected from GoM shoreline sites following the Deepwater Horizon blowout.

Data table header descriptions
ID_REF
VALUE Log2 RMA signal

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.359302846
AFFX-BioB-5_at 7.850515894
AFFX-BioB-M_at 7.865357038
AFFX-BioC-3_at 8.548916395
AFFX-BioC-5_at 8.663567678
AFFX-BioDn-3_at 11.23543609
AFFX-BioDn-5_at 9.973954433
AFFX-CreX-3_at 12.98686563
AFFX-CreX-5_at 12.30209707
AFFX-DapX-3_at 3.204637911
AFFX-DapX-5_at 3.358995931
AFFX-DapX-M_at 3.045790792
AFFX-Dr-AB076373-1_at 3.898762957
AFFX-Dr-acta1-3_at 14.80137662
AFFX-Dr-acta1-5_at 12.4505577
AFFX-Dr-acta1-5_x_at 13.42190407
AFFX-Dr-acta1-M_at 13.89129289
AFFX-Dr-AF292559-1_at 3.077248325
AFFX-Dr-AF292559-2_s_at 2.45172933
AFFX-Dr-AF292559-3_s_at 2.787289272

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM1277368_6.23_Control_72.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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